Many microbiome studies involve examining the microbiome in various samples and asking and answering "Are there differences in the microbiome between my sample types?". This is a standard correlative analysis used in all sorts of areas of science. and it can be quite useful in many cases.

However, in most cases it is not OK to take information from a correlative study and infer that the microbiome was "changed" due to some factor that differed between the samples. Generally this would only be possible to do in some sort of controlled experimental manipulation experiment. But so so so many people make such inferences and I am going to highlight an example that relates to a new study of vaping and the microbiome.

Basically the researchers compared microbiomes in three groups of people who had different behaviors (some non smokers, some smokers, some papers vapers). Note - they did not study people before and after vaping or smoking. They compared different people who differed in these behaviors but also differ in 100s to 1000s of other things like diet, gender, age, activity, housing, childhood, and more.

And when they did comparisons in relation to the main variables of non smoker, smoker, vaper, they found some differences in microbiomes and some similarities. Small study. But potentially interesting.

However, the PR significantly misrepresents what they did and found. Here are some examples of wording I have a problem with:

Press Release:

"Vapers and non-smokers have the same flourishing gut flora."

OK this has nothing to do with the point of my post but they do not in any way show "flourishing" flora.

"whilst smokers have significant changes to their microbiome".

No. They show differences. Not changes

Significant changes were found in the gut bacteria of the smokers, with an increase in the Prevotella bacteria which is linked to an increased risk of colon cancer and colitis.

Again. No. They show differences. They do not know if they are changes since they do not know what these people had before smoking. And thus they cannot show "increases" either.

There was also a decrease in the presence of Bacteroides in smokers, a beneficial bacteria or probiotic.

No - no decrease shown. And for that matter - not all Bacteroides are beneficial or probiotic.

More investigation is needed but to find that vaping is less-damaging than smoking on our gut bacteria adds to the incentive to change to e-cigarettes and for people to use them as a tool to quit smoking completely.

Jesus #(@(@. No. They did not show this.

This revealed significant changes in the gut bacteria of the faecal samples.

Monday, March 26, 2018

Made a Twitter moment that people may be interested in about a Buzzfeed article by Stephanie Lee on retraction of a deeply flawed paper supposedly connecting the Gut Makeover Diet to the microbiome and to beneficial health effects.

Monday, March 19, 2018

Well, I can't even begin to explain how disappointed I am in AAAS and Science Magazine over their actions recently. An "opinion" article was published last week in the "Working Life" section of Science which was stunningly inappropriate for Science Magazine.
I first found out about this when I saw a Tweet from a colleague and friend Rebecca Calisi Rodriguez.

I recently had a great experience publishing in @sciencemagazine's Working Life section on supporting mothers-in-science. Angry to see this now published- a personal, sexist attack on one woman (who is actually AWESOME at #Scicomm). A step back for #WomenInSTEM. Good thread here: https://t.co/KdVSqll3Rg

To sum up - the article was by a student who was apparently trying to express some thoughts about #SciComm activities by others that she did not like. And in the piece she named and mocked the activities of another PhD student at her own institution who does SciComm in ways she does not feel comfortable with. Fortunately, when I started looking at social media responses to this, they were overwhelmingly in support of this targeted student - Samantha Yammine who does really quite phenomenal SciComm work. (See for example her Twitter feed and her Instagram feed.

I am really thrilled and proud of the community that came out in support of her.

There have also been a few news stories related to or directly about the topic which are worth reading.

Also some of the Tweet streams about this are really worth reading. For example, this one from @christineliuart is a must read:

NEWS FLASH: my self-expression does not exist for you. Do not police the way I choose to interact with others and share my existence because it makes you bitter. You do you, but don't write an op-ed about why you dont want me doing me.https://t.co/kAMulZJ6vV

From my estimates there are 47 speakers of which 41 are male (note - these are inferences of gender and may be inaccurate). That comes out to an estimate of 87% male speakers. That is just not good. The microbiome field has a good sample pool of people of diverse backgrounds that could be speakers at meetings and thus meetings that are this skewed in diversity should not be supported.

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UPDATE 3/20/2018

The organizer of the meeting Mollie Roth has written to me to object to my post. She says she tried to have a more diverse collection of speakers. She says she invited many other women to speak, some who did not answer, and some who could not come, and some women who could not come sent men to replace them.

She wrote (I have removed names here)

XXX from YYY was committed to speak and had to drop out due to work commitments,

that XXX of YYY was invited to speak and declined,

that XXX of YYY was invited to speak and choose to send a man instead,

that XXX committed to speak and had to drop out due to other commitments and is sending a man instead

that XXX of YYY was invited and never responded

that XXX andXXX of YYY were invited and never responded

That’s 7 women off the top of my head without going into my files and pulling up all the ones that were invited and never responded or declined because they could not make it or accepted and ultimately sent a man from their companies instead. I wonder what that number alone would do to your stats?

I responded that I did not feel this was in any way sufficient but she disagrees. I pointed her to some suggestions for how to run a more diverse meeting that do not simply involve inviting more women to speak.

She also noted that she offended by my post and that I did not continue a private conversation we had on Linked In regarding this meeting. I note I did not continue the private conversation, and chose to post this post, because her response to my private critique made it seem that she was not interested in having a private conversation about the meeting.

-----------------------------
UPDATE 2. 3/20/2018 3 PM PST.

The organizer of the meeting Mollie Roth apparently thinks that I have deleted her "comment" on this blog. I have not done that. The 1st comment made to this blog is the one where she is accusing me of deleting a comment. I note - blog comments are open for anyone to post here for 2 weeks and then comments get moderated. I checked the Blogger SPAM comment filter but there is nothing there. So I can only conclude she did not make a comment. I emailed her to try to find out what she meant but she did not answer directly. I think what she may have meant is that she wanted me to post the full email of her communication with me to the blog but I am honestly not sure. I am pondering posting all my communications with her but am not sure if that is a good idea at this point.

So for now I am posting the entirety of her first message to me which I had edited a bit above. I am still editing out identifying features of others however. See below.

Professor EisenXXX was kind enough to forward your email to me encouraging him not to participate in the Arrowhead conference. Really? Rather than engaging in a conversation with me on LinkedIn and learning more about this year’s gender imbalance, you are posting about it on your blog and reaching out to speakers encouraging them to drop out. Would you care to take a moment to learn that -

XXX from YYY was committed to speak and had to drop out due to work commitments,

that XXX of YYY was invited to speak and declined,

that XXX of YYY was invited to speak and choose to send a man instead,

that XXX committed to speak and had to drop out due to other commitments and is sending a man instead

that XXX of YYY was invited and never responded

that XXX andXXX of YYY were invited and never responded

That’s 7 women off the top of my head without going into my files and pulling up all the ones that were invited and never responded or declined because they could not make it or accepted and ultimately sent a man from their companies instead. I wonder what that number alone would do to your stats?I will ask, although I am sure you will neither respond nor do the right thing, that you primarily stop contacting speakers to ask them not to participate. But secondarily you should really if not retract your offensive post add some of this information to inform it and perhaps encourage the women to own some of this issue themselves this year.I am sure you will do neither, unfortunately. I will be sure we do address this issue in our conference blog and in our social media channels.
----------------------------

UPDATE 3 3/20 11 PM PST

I guess my inclusion of this additional information was not enough for the organizer Mollie Roth. She seemed to imply that I was hiding her explanations from the public. So ... I am going to post them all here.

This all started with a Linked in message from her to me on March 5 telling me about this meeting.
I wrote back a few days later - obviously not enthusiastic about this meeting

She then wrote back, clearly not impressed with me. I am not sure if she would be OK with me posting all of the comments she made in that thread so I am just posting the most relevant one here which is how she ended the discussion.

Sounded to me like she did not want anything to do with me ever again. I pondered what to do for a while. Was writing back a good or a bad thing? I did not know. But I decided to try. I wrote a response and tried to send it but the message would not go through. I assumed she blocked me or disconnected / delinked me (I don't know what that is called on Linkedin). I thought about emailing her back but the last message from her implied to me that she wanted nothing more to do with me.

So a few days later I wrote a blog post about YAMMMMs in relation to this meeting. And then I wrote this blog post here. And then I engages in some discussion about the post on Twitter and asked some of the speakers to not speak at the meeting. I emailed one that I knew well and he forwarded the email to Mollie. She then sent me an email. I have deleted names and other identifying features of other people from this and other messages.

------------------------------

Professor Eisen

XXX was kind enough to forward your email to me encouraging him not to participate in the Arrowhead conference.

Really? Rather than engaging in a conversation with me on LinkedIn and learning more about this year’s gender imbalance, you are posting about it on your blog and reaching out to speakers encouraging them to drop out.

Would you care to take a moment to learn that - XXX from YYY was committed to speak and had to drop out due to work commitments,

that XXX of YYY was invited to speak and declined,

that XXX of YYY was invited to speak and choose to send a man instead,

that XXX committed to speak and had to drop out due to other commitments and is sending a man instea

that XXX of YYY was invited and never respondedthat XXX and XXX of YYY were invited and never responded

That’s 7 women off the top of my head without going into my files and pulling up all the ones that were invited and never responded or declined because they could not make it or accepted and ultimately sent a man from their companies instead. I wonder what that number alone would do to your stats?

I will ask, although I am sure you will neither respond nor do the right thing, that you primarily stop contacting speakers to ask them not to participate. But secondarily you should really if not retract your offensive post add some of this information to inform it and perhaps encourage the women to own some of this issue themselves this year

I am sure you will do neither, unfortunately. I will be sure we do address this issue in our conference blog and in our social media channels.

MollieMollie Roth, J.D.Managing PartnerPGx Consulting

-----------------------

I wrote back

Mollie

In our conversation on Linked In you basically told me you were not interested in discussing the issue. Your last message was "I am sorry I reached out to you and will not make the mistake of doing so again. Good day."

Regardless, I tried to write back but was unable to respond to you via the messaging system. I assumed that was because you blocked me in some way.

Given that you did not seem to want to discuss it further in private, I decided to take it public. I would be more than happy to add whatever response you want to my blog post or you can post there. I stand by my critique of your meeting. It is not enough to just invite a few women to speak in my opinion and there is much literature on this out there if you are interested. In order to achieve a diverse meeting one must work a bit more on it. If you are interested in suggestions for how to do this, please see this part of my blog.https://phylogenomics.blogspot.com/p/posts-on-women-in-science.html

Jonathan

-----------------------

She then wrote back

Jonathan

I neither blocked you nor impeded your communication in any way on LinkedIn or anywhere else. I have my doubts that you are so easily put off, I think you prefer the hype and hyperbole of being the individual who “outs” the bad actors, regardless of whether they are or they are not.

I take offense at your characterization that I did no more than invite a few women, I do substantial research and go well beyond a bald faced email with no followup. I know many of these women personally from interactions over the years from prior conferences - where we have agreed women were well represented - but saying my conference fails on this front from a single year is a slant helpful only to you.

I will be more than happy to have you demonstrate your acuity with gathering these women and getting them to the table next year. Writing about these issues from an academic perspective is one thing, actually driving engagement is quite another.

In fact I will be more than happy to make a space for you on the podium this year if you would like to come speak about these issues and commit to lending your knowledgeable hand as a consultant next year to demonstrate how these “suggestions” work in practice. What say you Professor Eisen, willing to put your academic suggestions to the test in the real world?

So I responded

Mollie

In your 1st communication with me in September of 2015, you wrote

"Let me start by applauding you for the commentary in your blog post on overselling the microbiome about the gender imbalance in Dr. Roizen’s conference. "

So back then you supported a public critique of a meeting in relation to its gender balance of speakers. This is why I wrote back to you privately on Linked In in such a shocked state regarding your current meeting.

So -what has changed since then? Your meeting has an unbalanced gender for speakers. And I bogged about it. Just like I did previously and which you applauded me for.

Again, I stand by my critique of your meeting. And no, I am definitely not interested in attending it in any way or for any purpose. And I will continue to recommend other people not attend it or speak at it as it now stands. If you run a meeting with a better gender balance I would be more than happy to participate in some way in a discussion of gender issues in STEM.

She wrote back

It is not until one is unfairly targeted that one understands how skewed people pointing these types of things out are. Knowing what I know now about your skewed attacks, I was perhaps unfair in assuming others were acting in bad faith. I d not believe you are acting in good faith, nor do I believe you will do so. I think you like the fight, I think you like the hyperbole and I think you like pointing fingers with no intention of trying to understand the other side.

I wrote back

Ok.

Believe what you want.

I still welcome any comments you would like to make on my blog and whether you believe it or not I truly believed you did not want to hear a anything more from me in private. I certainly could have made more of an effort to figure that out. But your response led me to believe that that path was closed.

Molly wrote

If you were sincere Professor Eisen you would amend or include further information you have been provided on your blog post yourself. Of course I am going to contradict what you said or have a different perspective but it really only has substantial meaning if you are willing to say “ok hang on, here are some things I did not know” and further inform the conversation yourself.

I will get in touch with our speakers and let them know the nature of your communications and how you have refused to take the information you have been provided and adjust your outrage.

So I decided to do what she asked. It seemed only fair. And I updated my post with a summary of her comments. I did not say I agreed with her but I did try to provide her perspective.

I thought I was doing what she asked. To give her side of the story. I did not think I was obliged to agree with her but she then wrote back something which I just do not understand.

I just went to remove my response to your post realizing the fact that you are not really interested din the reality of these situations to find you had removed it and, no surprise, recharacterized it all in your own words. That’s not open discourse Professor Eisen now is it, more evidence that you simply like being the finger pointer and are not actually interested in honest and open engagement.

This was so strange because she never posted a comment to my blog. I went and checked SPAM and comments awaiting moderation and -- nothing. I was very very confused. So I wrote back

Mollie

I have no idea what you are talking about here.

When did you write a response and post it to my blog? Did you submit a comment? I have no record of that. How could you then remove it? How could I then remove it? You have not as far as I know posted any comment anywhere. I have certainly not removed a single thing you posted to my blog nor would I.

She then wrote

Oh my goodness. You literally wrote on your blog that the organizer responded on your blog and then recharacterized what I said and you are now playing DUMB?

So so weird. I did not delete any comment. She never made any comment. And now her explanation what that she was claiming I had written that she made a comment. But I did not write that. My guess is she either (1) thought that her email to me was automatically posted to my blog (seems unlikely that she thought that) or (2) that I had posted her comments to my blog directly and then deleted them. Seemed like 2 was the only plausible option But since she had already told me she did not want me to post her comments directly to my blog this seemed weird. So I wrote back again.

No Mollie

I wrote "The organizer of the meeting Mollie Roth has written to me to object to my post"I did not say you wrote on my blog.

And when I asked you in email if I should post your comments to my blog directly you wrote

"If you were sincere Professor Eisen you would amend or include further information you have been provided on your blog post yourself. Of course I am going to contradict what you said or have a different perspective but it really only has substantial meaning if you are willing to say “ok hang on, here are some things I did not know” and further inform the conversation yourself. "

Clearly saying you did not want me to just post what you wrote.

I did not hear back immediately so I wrote a follow up:

Here is a proposal. I will post the entire contents of these emails to my blog in the interest of transparency. Are you OK with that?

And she wrote back:

It is your blog Professor, you are free to do with it anything you wish, clearly

So here we are. I still do not know what she meant by me deleting her comments from my blog, which I did not do. But in the interest of transparency I am posting all of our emails here.

--------------------------

UPDATE 4. 3/21/18

Mollie Roth, the organizer of the meeting sent an email to all the speakers of the meeting and cc'd me. In the interest of transparency, especially since she accused me of deleting comments that she never posted here, I feel comfortable posting her email here.

Dear Speakers

It has come to our attention that you may have received a message from a Professor Jonathan Eisen at UC Davis encouraging you to boycott the Arrowhead conference next month because of the lack of gender diversity on the speaking faculty.

Unfortunately Professor Eisen is absolutely correct, the speaking faculty is predominantly male this year. Highlighting the role of women in this industry has been a top priority since I started this conference four years ago and prior years were much more gender balanced. Professor Eisen is well aware of this from our prior discussions on the issue. His dissatisfaction this year is equal to mine - in spite off having identified and invited numerous women to speak, they did not respond to my invitation or accepted and subsequently had to withdraw or in two cases decided to send men in their places.Several of you have been in touch asking what WE are going to do to address this issue. I will turn that question around as gender diversity in the sciences is all of our responsibility - what are YOU going to do to address this?

I encourage all of you to identify a women in your organization and send her to speak in your place if this issue is of concern to you. There is only so much I can do as an outsider to drive this issue, it requires everyone working together.

If this is possible, please let us know as soon as possible and we will switch out her name and bio for yours on the online agenda and before it goes to press for printing. It would be my great pleasure to highlight this happening next month.

And I will extend the same invitation to Professor Eisen who is copied here that I did privately, please consider lending your substantial knowledge and expertise on this issue to making this gender diversity happen not simply in your academic writing but in the real world. I welcome your time and assistance in pulling together the faculty for the conference next year. The experience will no doubt further inform your understanding of just how difficult this task is to accomplish in the real world.

If you have any questions or continuing concerns, please do not hesitate to be in touch.

Thank you very much for working to improve the diversity of speakers at this meeting. I think asking for help in identifying and selecting speakers that represent a broader sample of diversity is a great idea. In addition, I would be more than happy to help you organize a conference next year.

Contrary to your comments, I have extensive experience planning and running conferences in various STEM area including the microbiome space. And though it can be difficult to achieve, for these we have had excellent diversity of speakers. You can see a partial list here.

For each of the meetings I have organized in the last 5 or so years (I became interested to speaker diversity about 10 years ago but have been more committed to it in the last 5) we have been able to achieve a strong representation of diversity among the speakers. This is however not easy in every case and takes a strong commitment to diversity and sometimes significant amounts of work.

Develop a diversity policy and publicly post it stating your commitment to diversity for speakers. I would be happy to help you develop one. Many people basically copy a template that has come up from the technology world. I note this should not just be about gender diversity but about diversity broadly (i.e., racial, ethnic, gender, career stage, background, country, type of institution, etc). An example is https://us.pycon.org/2017/about/diversity/

When people turn down invitations, ask them why and whether you could do anything to make it more likely the next time for them to accept. It may be that some simple changes might make it more likely for people to accept.

Broaden the invitation pool by expanding topics or types of people you invite. This could, for example, include having a student or post doc presentation in each session, or including sessions focused on related topics such as press coverage of the field, or such.

Ask people in the field for help in identifying speakers. Ideally this would happen at the planning stage but could happen any time.